Abstract: SSR molecular markers which had the technical advantages of fast, stable and accurate were used to investigate the genetic diversity and purity test of two hybrid seed commercially available. 36 rice SSR primer pairs were used to assess the genetic diversity of 38 hybrid rice samples. The result showed two of the sample were heterogenous (genetic distance 0.11), whereas two of the others seemed to be synonym (genetic distance 0.03). 33 maize SSR primer pairs were used to determine the genetic diversity of 36 hybrid maize sample, the result showed two of the sample were heterogenous (genetic distance 0.12). In the artificial mixed sample test, u test revealed there was no significant difference between all sample test value and actual mixed ratio. Meanwhile, 10 hybrid rice samples provided by seed company were compared with SSR molecular marker and field identification methods, though SSR marker test results were below the field identification in three samples, the field identifying were on the basis of agronomic traits, it was difficult to distinguish the similar genetic background strains, it indicated that SSR molecular marker was more favorable than the other detection methods.